X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Ffts%2Fservice%2Fpdb%2FPDBFTSRestClient.java;h=d8ab7de02f422433241aa52fc2d052088d32873a;hb=ee6db3e52520d26acea3f68886dd05b89c86b76f;hp=6e097dd3139266439bbe83e467a92aef52dffacf;hpb=007af0c9001900071f6d8e9214143f79e10f4938;p=jalview.git diff --git a/src/jalview/fts/service/pdb/PDBFTSRestClient.java b/src/jalview/fts/service/pdb/PDBFTSRestClient.java index 6e097dd..d8ab7de 100644 --- a/src/jalview/fts/service/pdb/PDBFTSRestClient.java +++ b/src/jalview/fts/service/pdb/PDBFTSRestClient.java @@ -29,6 +29,7 @@ import jalview.fts.core.FTSRestRequest; import jalview.fts.core.FTSRestResponse; import jalview.util.MessageManager; +import java.net.URI; import java.util.ArrayList; import java.util.Collection; import java.util.Iterator; @@ -42,15 +43,24 @@ import org.json.simple.JSONObject; import org.json.simple.parser.JSONParser; import org.json.simple.parser.ParseException; +//import jalview.javascript.web.Client; +//import jalview.javascript.web.ClientResponse; +//import jalview.javascript.web.WebResource; + import com.sun.jersey.api.client.Client; import com.sun.jersey.api.client.ClientResponse; import com.sun.jersey.api.client.WebResource; + import com.sun.jersey.api.client.config.ClientConfig; import com.sun.jersey.api.client.config.DefaultClientConfig; /** * A rest client for querying the Search endpoint of the PDB API * + * BH 2018: just a tiny tweak here - for SwingJS, we coerce the classes to be + * from jalview.javascript.web instead of com.sun.jersey.api.client + * + * * @author tcnofoegbu * */ @@ -59,7 +69,7 @@ public class PDBFTSRestClient extends FTSRestClient private static FTSRestClientI instance = null; - public static final String PDB_SEARCH_ENDPOINT = "http://www.ebi.ac.uk/pdbe/search/pdb/select?"; + public static final String PDB_SEARCH_ENDPOINT = "https://www.ebi.ac.uk/pdbe/search/pdb/select?"; protected PDBFTSRestClient() { @@ -73,19 +83,22 @@ public class PDBFTSRestClient extends FTSRestClient * @return the pdbResponse object for the given request * @throws Exception */ + @SuppressWarnings({ "unused", "unchecked" }) @Override public FTSRestResponse executeRequest(FTSRestRequest pdbRestRequest) throws Exception { try { - ClientConfig clientConfig = new DefaultClientConfig(); - Client client = Client.create(clientConfig); + Client client; + WebResource webResource; - String wantedFields = getDataColumnsFieldsAsCommaDelimitedString(pdbRestRequest - .getWantedFields()); - int responseSize = (pdbRestRequest.getResponseSize() == 0) ? getDefaultResponsePageSize() + String wantedFields = getDataColumnsFieldsAsCommaDelimitedString( + pdbRestRequest.getWantedFields()); + int responseSize = (pdbRestRequest.getResponseSize() == 0) + ? getDefaultResponsePageSize() : pdbRestRequest.getResponseSize(); + int offSet = pdbRestRequest.getOffSet(); String sortParam = null; if (pdbRestRequest.getFieldToSortBy() == null || pdbRestRequest.getFieldToSortBy().trim().isEmpty()) @@ -107,11 +120,11 @@ public class PDBFTSRestClient extends FTSRestClient } } - String facetPivot = (pdbRestRequest.getFacetPivot() == null || pdbRestRequest - .getFacetPivot().isEmpty()) ? "" : pdbRestRequest - .getFacetPivot(); - String facetPivotMinCount = String.valueOf(pdbRestRequest - .getFacetPivotMinCount()); + String facetPivot = (pdbRestRequest.getFacetPivot() == null + || pdbRestRequest.getFacetPivot().isEmpty()) ? "" + : pdbRestRequest.getFacetPivot(); + String facetPivotMinCount = String + .valueOf(pdbRestRequest.getFacetPivotMinCount()); String query = pdbRestRequest.getFieldToSearchBy() + pdbRestRequest.getSearchTerm() @@ -121,13 +134,31 @@ public class PDBFTSRestClient extends FTSRestClient : " AND status:REL"); // Build request parameters for the REST Request - WebResource webResource = null; + + // BH 2018 the trick here is to coerce the classes in Javascript to be + // different from the ones in Java yet still allow this to be correct for Java + Class clientResponseClass; + if (/** @j2sNative true || */ + false) + { + // JavaScript only -- coerce types to Java types for Java + client = (Client) (Object) new jalview.javascript.web.Client(); + clientResponseClass = (Class) (Object) jalview.javascript.web.ClientResponse.class; + } + else + { + // Java only + client = Client.create(new DefaultClientConfig()); + clientResponseClass = ClientResponse.class; + } + if (pdbRestRequest.isFacet()) { webResource = client.resource(PDB_SEARCH_ENDPOINT) .queryParam("wt", "json").queryParam("fl", wantedFields) .queryParam("rows", String.valueOf(responseSize)) .queryParam("q", query) + .queryParam("start", String.valueOf(offSet)) .queryParam("sort", sortParam).queryParam("facet", "true") .queryParam("facet.pivot", facetPivot) .queryParam("facet.pivot.mincount", facetPivotMinCount); @@ -137,12 +168,15 @@ public class PDBFTSRestClient extends FTSRestClient webResource = client.resource(PDB_SEARCH_ENDPOINT) .queryParam("wt", "json").queryParam("fl", wantedFields) .queryParam("rows", String.valueOf(responseSize)) - .queryParam("q", query) - .queryParam("sort", sortParam); + .queryParam("start", String.valueOf(offSet)) + .queryParam("q", query).queryParam("sort", sortParam); } + + URI uri = webResource.getURI(); + // Execute the REST request - ClientResponse clientResponse = webResource.accept( - MediaType.APPLICATION_JSON).get(ClientResponse.class); + ClientResponse clientResponse = webResource + .accept(MediaType.APPLICATION_JSON).get(clientResponseClass ); // Get the JSON string from the response object String responseString = clientResponse.getEntity(String.class); @@ -159,8 +193,8 @@ public class PDBFTSRestClient extends FTSRestClient } else { - errorMessage = getMessageByHTTPStatusCode(clientResponse - .getStatus()); + errorMessage = getMessageByHTTPStatusCode( + clientResponse.getStatus(), "PDB"); throw new Exception(errorMessage); } } @@ -178,16 +212,14 @@ public class PDBFTSRestClient extends FTSRestClient if (exceptionMsg.contains("SocketException")) { // No internet connection - throw new Exception( - MessageManager - .getString("exception.unable_to_detect_internet_connection")); + throw new Exception(MessageManager.getString( + "exception.unable_to_detect_internet_connection")); } else if (exceptionMsg.contains("UnknownHostException")) { // The server 'www.ebi.ac.uk' is unreachable - throw new Exception( - MessageManager - .getString("exception.pdb_server_unreachable")); + throw new Exception(MessageManager.formatMessage( + "exception.fts_server_unreachable", "PDB Solr")); } else { @@ -196,36 +228,6 @@ public class PDBFTSRestClient extends FTSRestClient } } - public String getMessageByHTTPStatusCode(int code) - { - String message = ""; - switch (code) - { - case 410: - message = MessageManager - .getString("exception.pdb_rest_service_no_longer_available"); - break; - case 403: - case 404: - message = MessageManager.getString("exception.resource_not_be_found"); - break; - case 408: - case 409: - case 500: - case 501: - case 502: - case 503: - case 504: - case 505: - message = MessageManager.getString("exception.pdb_server_error"); - break; - - default: - break; - } - return message; - } - /** * Process error response from PDB server if/when one occurs. * @@ -238,6 +240,26 @@ public class PDBFTSRestClient extends FTSRestClient StringBuilder errorMessage = new StringBuilder( "\n============= PDB Rest Client RunTime error =============\n"); + +// { +// "responseHeader":{ +// "status":0, +// "QTime":0, +// "params":{ +// "q":"(text:q93xj9_soltu) AND molecule_sequence:['' TO *] AND status:REL", +// "fl":"pdb_id,title,experimental_method,resolution", +// "start":"0", +// "sort":"overall_quality desc", +// "rows":"500", +// "wt":"json"}}, +// "response":{"numFound":1,"start":0,"docs":[ +// { +// "experimental_method":["X-ray diffraction"], +// "pdb_id":"4zhp", +// "resolution":2.46, +// "title":"The crystal structure of Potato ferredoxin I with 2Fe-2S cluster"}] +// }} +// try { JSONParser jsonParser = new JSONParser(); @@ -289,8 +311,8 @@ public class PDBFTSRestClient extends FTSRestClient .parse(pdbJsonResponseString); JSONObject pdbResponse = (JSONObject) jsonObj.get("response"); - String queryTime = ((JSONObject) jsonObj.get("responseHeader")).get( - "QTime").toString(); + String queryTime = ((JSONObject) jsonObj.get("responseHeader")) + .get("QTime").toString(); int numFound = Integer .valueOf(pdbResponse.get("numFound").toString()); if (numFound > 0) @@ -327,8 +349,9 @@ public class PDBFTSRestClient extends FTSRestClient Collection diplayFields = request.getWantedFields(); SequenceI associatedSeq = request.getAssociatedSequence(); int colCounter = 0; - summaryRowData = new Object[(associatedSeq != null) ? diplayFields - .size() + 1 : diplayFields.size()]; + summaryRowData = new Object[(associatedSeq != null) + ? diplayFields.size() + 1 + : diplayFields.size()]; if (associatedSeq != null) { associatedSequence = associatedSeq; @@ -353,15 +376,17 @@ public class PDBFTSRestClient extends FTSRestClient { try { - summaryRowData[colCounter++] = (field.getDataColumnClass() == Integer.class) ? Integer - .valueOf(fieldData) - : (field.getDataColumnClass() == Double.class) ? Double - .valueOf(fieldData) - : fieldData; + summaryRowData[colCounter++] = (field.getDataType() + .getDataTypeClass() == Integer.class) + ? Integer.valueOf(fieldData) + : (field.getDataType() + .getDataTypeClass() == Double.class) + ? Double.valueOf(fieldData) + : sanitiseData(fieldData); } catch (Exception e) { e.printStackTrace(); - System.out.println("offending value:" + fieldData); + System.out.println("offending value:" + fieldData); } } } @@ -407,16 +432,29 @@ public class PDBFTSRestClient extends FTSRestClient { return Objects.hash(primaryKey1, this.toString()); } + + @Override + public boolean equals(Object that) + { + return this.toString().equals(that.toString()); + } }; } + private static String sanitiseData(String data) + { + String cleanData = data.replaceAll("\\[\"", "").replaceAll("\\]\"", "") + .replaceAll("\\[", "").replaceAll("\\]", "") + .replaceAll("\",\"", ", ").replaceAll("\"", ""); + return cleanData; + } + @Override public String getColumnDataConfigFileName() { - return getResourceFile("fts/pdb_data_columns.conf"); + return "/fts/pdb_data_columns.txt"; } - public static FTSRestClientI getInstance() { if (instance == null) @@ -425,4 +463,44 @@ public class PDBFTSRestClient extends FTSRestClient } return instance; } + + private Collection allDefaultDisplayedStructureDataColumns; + + public Collection getAllDefaultDisplayedStructureDataColumns() + { + if (allDefaultDisplayedStructureDataColumns == null + || allDefaultDisplayedStructureDataColumns.isEmpty()) + { + allDefaultDisplayedStructureDataColumns = new ArrayList(); + allDefaultDisplayedStructureDataColumns + .addAll(super.getAllDefaultDisplayedFTSDataColumns()); + } + return allDefaultDisplayedStructureDataColumns; + } + + public static void main(String[] args) { + + + String s = "e"; + + + char c = 'c'; + char f = 'f'; + s += c | f; + int x = c&f; + int y = 2 & c; + int z = c ^ 5; + JSONParser jsonParser = new JSONParser(); + try + { + JSONObject jsonObj = (JSONObject) jsonParser.parse("{\"a\":3}"); + System.out.println(jsonObj); + } catch (ParseException e) + { + e.printStackTrace(); + } + + } + + }